In your wave editing software, when you created the test tone, in the "save" screen, was there an extra check box that you checked?
The check box would have said something like "Save extra non-audio information", or "Append track details to file", or something like that.
This would append a piece of ASCII text data to the end of the file, which, when processed by a piece of wave playback software or an MP3 encoder, would cause a click.
The solution is to create the file without the extra appended data.